scholarly journals Transcriptomics Analysis of Lens from Patients with Posterior Subcapsular Congenital Cataract

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1904
Author(s):  
Xiaolei Lin ◽  
Hongzhe Li ◽  
Tianke Yang ◽  
Xin Liu ◽  
Fan Fan ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Differentially Expressed Genes ◽  
Congenital Cataract ◽  
Fold Change ◽  
Differentially Expressed ◽  
P Value ◽  
Sequencing Analysis ◽  
Log2 Fold Change ◽  
Upregulated Genes ◽  
Cataract Patients

To gain insight into the aetiology of posterior subcapsular congenital cataract from the perspective of transcriptional changes, we conducted an mRNA sequencing analysis of the lenses in posterior subcapsular congenital cataract patients and in normal children. There were 1,533 differentially expressed genes from 19,072 genes in the lens epithelial cells of the posterior subcapsular congenital cataract patients compared to in the normal controls at a cut-off criteria of |log2 fold change| of >1 and a p-value of <0.05, including 847 downregulated genes and 686 upregulated genes. To further narrow down the DEGs, we utilised the stricter criteria of |log2 fold change| of >1 and an FDR value of <0.05, and we identified 551 DEGs, including 97 upregulated genes and 454 downregulated genes. This study also identified 1,263 differentially expressed genes of the 18,755 genes in lens cortex and nuclear fibres, including 646 downregulated genes and 617 upregulated genes. The downregulated genes in epithelial cells were significantly enriched in the structural constituent of lenses, lens development and lens fibre cell differentiation. After filtering the DEGs using the databases iSyTE and Cat-Map, several high-priority candidate genes related to posterior subcapsular congenital cataract such as GRIFIN, HTRA1 and DAPL1 were identified. The findings of our study may provide a deeper understanding of the mechanisms of posterior subcapsular congenital cataract and help in the prevention and treatment of this disease.

Identification of Differentially Expressed and Spliced Genes with RNA Sequencing Analysis of CLL Specimens

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 4582-4582
Author(s):  
Wei Liao ◽  
Gwen Jordaan ◽  
Artur Jaroszewicz ◽  
Matteo Pellegrini ◽  
Sanjai Sharma
Keyword(s):  
B Cells ◽  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
Fold Change ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
Sequencing Analysis ◽  
Rna Seq ◽  
Mrna Isoforms ◽  
Core Set

Abstract Abstract 4582 High throughput sequencing of cellular mRNA provides a comprehensive analysis of the transcriptome. Besides identifying differentially expressed genes in different cell types, it also provides information of mRNA isoforms and splicing alterations. We have analyzed two CLL specimens and a normal peripheral blood B cells mRNA by this approach and performed data analysis to identify differentially expressed and spliced genes. The result showed CLLs specimens express approximately 40% more transcripts compared to normal B cells. The FPKM data (fragment per kilobase of exon per million) revealed a higher transcript expression on chromosome 12 in CLL#1 indicating the presence of trisomy 12, which was confirmed by fluorescent in-situ hybridization assay. With a two-fold change in FPKM as a cutoff and a p value cutoff of 0.05 as compared to the normal B cell control, 415 genes and 174 genes in CLL#1 and 676 and 235 genes in CLL#2 were up and downregulated or differentially expressed. In these two CLL specimens, 45% to 75% of differentially expressed genes are common to both the CLL specimens indicating that genetically disparate CLL specimens have a high percentage of a core set of genes that are potentially important for CLL biology. Selected differentially expressed genes with increased expression (selectin P ligand, SELPLG, and adhesion molecule interacts with CXADR antigen 1, AMICA) and decreased (Fos, Jun, CD69 and Rhob) expression based on the FPKM from RNA-sequencing data were also analyzed in additional CLL specimens by real time PCR analysis. The expression data from RNA-seq closely matches the fold-change in expression as measured by RT-PCR analysis and confirms the validity of the RNA-seq analysis. Interestingly, Fos was identified as one of the most downregulated gene in CLL. Using the Cufflinks and Cuffdiff software, the splicing patterns of genes in CLL specimens and normal B cells were analyzed. Approximately, 1100 to 1250 genes in the two CLL specimens were significantly differentially spliced as compared to normal B cells. In this analysis as well, there is a core set of 800 common genes which are differentially spliced in the two CLL specimens. The RNA-sequencing analysis accurately identifies differentially expressed novel genes and splicing variations that will help us understand the biology of CLL. Disclosures: No relevant conflicts of interest to declare.

P135 MAJOR GENE REGULATORS AFFECTED IN COLON AND BLOOD OF DEXTRAN SODIUM SULFATE ACUTE COLITIS MURINE MODEL

2020 ◽  
Vol 26 (Supplement_1) ◽  
pp. S32-S32
Author(s):  
Reza Yarani ◽  
Oana Palasca ◽  
Nadezhda Tsankova Doncheva ◽  
Christian Anthon ◽  
Bartosz Pilecki ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Intestinal Inflammation ◽  
Major Gene ◽  
Clinical Manifestations ◽  
Ease Of Use ◽  
Differentially Expressed ◽  
In Vivo Studies ◽  
P Value ◽  
Sequencing Analysis

Abstract Background Dextran sulfate sodium (DSS) ulcerative colitis (UC) murine models have long been used for in vivo studies. DSS is a negatively charged polysaccharide with colitogenic properties. Although the mechanisms by which DSS induces intestinal inflammation are not fully understood, there are several good reasons why the DSS chemical colitis model for investigating the immunopathogenesis mechanism of UC is widely used. These include strong phenotypic clinical manifestations which emulate numerous clinical and histopathological features of human UC, ease of use, low mortality rate and high reproducibility. Here, by using high-throughput RNA sequencing analysis we set to investigate the major predicted gene regulators (GRs) affected by differentially expressed genes in the DSS treated UC model in order to obtain regulatory insights into the pathogenic mechanisms of UC development. Methods A DSS-induced mouse model of UC was established. Total RNA from colon tissue and blood of 3 healthy and 3 DSS-treated mice was extracted and sequenced by Illumina HiSeq 4000. Gene expression levels were obtained by mapping and quantification to the annotated mouse genome. Subsequently, differential gene expression analysis between DSS-treated and control mice both in colon and blood was performed. Ingenuity pathway analysis software (IPA®, Qiagen) was used to predict/identify major GRs affected by significantly differentially expressed genes (SDEGs, FC &gt; |2|, p ≤0.05) in both colon and blood. Results Our analysis revealed how many and which major GRs are affected in DSS-treated mice and also the direction of change as compared to healthy (untreated) mice. In colon, 595 activated and 198 inhibited major GRs (p-value of overlap ≤0.05) in relation to ∼ 3180 SDEGs were identified, while in blood, we identified 205 activated and 62 inhibited GRs (in relation to ∼650 SDEGs). Colon and blood share 181 activated and 41 inhibited GRs. Identified GRs include transcription regulators, cytokines, transmembrane receptors and enzymes that mainly contribute to the development of inflammatory/immune responses. In colon and blood, the top 10 activated and inhibited regulators with the highest positive and negative activation z-score with target molecules as well as expression in the datasets are indicated in Figure 1a and 1b, respectively. Conclusion In this study, we analyzed linkage of GRs to SDEGs through coordinated expression and identified potential major regulators that have significant effect on UC pathogenic-related gene expression. These GRs seem to be the key regulators of transcriptomic changes induced by inflammation. These findings expand our molecular understanding of putative new targets that may be important in the pathophysiology of UC and provide biological insights into the observed expression changes between the UC and healthy controls.

scholarly journals 12 Survival-related differentially expressed genes based on the TARGET-osteosarcoma database

2021 ◽  
pp. 153537022110074
Author(s):  
Emel Rothzerg ◽  
Jiake Xu ◽  
David Wood ◽  
Sulev Kõks
Keyword(s):  
Differentially Expressed Genes ◽  
Clinical Information ◽  
Differentially Expressed ◽  
P Value ◽  
Sequencing Data ◽  
Gene Expressions ◽  
Expression Of Genes ◽  
Kaplan Meier ◽  
And Gender ◽  
Upregulated Genes

The Therapeutically Applicable Research to Generate Effective Treatments (TARGET) project aims to determine molecular changes that drive childhood cancers, including osteosarcoma. The main purpose of the program is to use the open-source database to develop novel, effective, and less toxic therapies. We downloaded TARGET-OS RNA-Sequencing data through R studio and merged the mRNA expression of genes with clinical information (vital status, survival time and gender). Further, we analyzed differential gene expressions between dead and alive patients based on TARGET-OS project. By this study, we found 5758 differentially expressed genes between deceased and alive patients with a false discovery rate below 0.05; 4469 genes were upregulated in deceased patients compared to alive, whereas 1289 genes were downregulated. The survival-related genes were obtained using Kaplan–Meier survival analysis and Cox univariate regression (KM < 0.05 and Cox P-value < 0.05). Out of 5758 differentially expressed genes, only 217 have been associated with overall survival. Eight survival-related downregulated genes ( ERCC4, CLUAP1, CTNNBIP1, GCA, RAB40C, SIRPA, USP11, and TCN2) and four survival-related upregulated genes ( MUC1, COL13A1, JAG2 and KAZALD1) were selected for further analysis as potential independent prognostic candidate genes. This study may help to discover novel prognostic markers and potential therapeutic targets for osteosarcoma.

scholarly journals Spermatozoa induce transcriptomic alterations in bovine oviductal epithelial cells prior to initial contact

2020 ◽  
Vol 14 (4) ◽  
pp. 439-451
Author(s):  
Qurat Ul Ain Reshi ◽  
Janeli Viil ◽  
James Ord ◽  
Freddy Lättekivi ◽  
Kasun Godakumara ◽  
...  
Keyword(s):  
Gene Expression ◽  
Epithelial Cells ◽  
Differentially Expressed Genes ◽  
Culture System ◽  
Contact System ◽  
Physical Contact ◽  
Differentially Expressed ◽  
Sequencing Analysis ◽  
Transcriptional Responses ◽  
Culture Model

Abstract The capability of spermatozoa to directly influence maternal gene expression is already established. Indeed, some of the changes induced by spermatozoa may have a direct functional importance in the pre-conceptional period. Although the mechanisms underlying these sperm-maternal interactions are not well characterized, it is possible that they could involve ligands that are released from the spermatozoa. This study therefore aimed to test whether physical contact between bovine spermatozoa and bovine oviductal epithelial cells (BOECs) is a prerequisite for spermatozoa-induced gene expression changes. We used two co-culture models: a contact co-culture model in which spermatozoa interact directly with BOECs, and a non-contact co-culture model in which an insert with the pore size of 0.4 μm was placed between spermatozoa and BOECs. Messenger RNA sequencing analysis of BOECs by RNA-seq revealed ten differentially expressed genes in contact system and 108 differentially expressed genes in the non-contact system after 10 h of co-culture. Retinol metabolism pathway and ovarian steroidogenesis pathway were significantly enriched in the non-contact co-culture system. Q-PCR analysis revealed that transcriptional responses can be rapid, with increased expression of four genes (DHRS3, CYP1B1, PTGS2, and ATF3) detectable within just 90 min of co-incubation, but with expression levels highly dependent on the type of co-culture system. The findings from our study demonstrate that direct contact with spermatozoa is not necessary to induce changes in gene expression of oviductal epithelial cells, suggesting that spermatozoa may be able to signal to maternal tissues in advance of their arrival.

scholarly journals Transcriptome analysis identifies differentially expressed genes in the progenies of a cross between two low phytic acid soybean mutants

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hangxia Jin ◽  
Xiaomin Yu ◽  
Qinghua Yang ◽  
Xujun Fu ◽  
Fengjie Yuan
Keyword(s):  
Developmental Stage ◽  
Phytic Acid ◽  
Differentially Expressed Genes ◽  
Transcriptome Analysis ◽  
Defense Mechanisms ◽  
Developmental Stages ◽  
Sucrose Metabolism ◽  
Differentially Expressed ◽  
Sequencing Analysis ◽  
Seed Developmental Stage

AbstractPhytic acid (PA) is a major antinutrient that cannot be digested by monogastric animals, but it can decrease the bioavailability of micronutrients (e.g., Zn and Fe). Lowering the PA content of crop seeds will lead to enhanced nutritional traits. Low-PA mutant crop lines carrying more than one mutated gene (lpa) have lower PA contents than mutants with a single lpa mutant gene. However, little is known about the link between PA pathway intermediates and downstream regulatory activities following the mutation of these genes in soybean. Consequently, we performed a comparative transcriptome analysis using an advanced generation recombinant inbred line with low PA levels [2mlpa (mips1/ipk1)] and a sibling line with homozygous non-mutant alleles and normal PA contents [2MWT (MIPS1/IPK1)]. An RNA sequencing analysis of five seed developmental stages revealed 7945 differentially expressed genes (DEGs) between the 2mlpa and 2MWT seeds. Moreover, 3316 DEGs were associated with 128 metabolic and signal transduction pathways and 4980 DEGs were annotated with 345 Gene Ontology terms related to biological processes. Genes associated with PA metabolism, photosynthesis, starch and sucrose metabolism, and defense mechanisms were among the DEGs in 2mlpa. Of these genes, 36 contributed to PA metabolism, including 22 genes possibly mediating the low-PA phenotype of 2mlpa. The expression of most of the genes associated with photosynthesis (81 of 117) was down-regulated in 2mlpa at the late seed developmental stage. In contrast, the expression of three genes involved in sucrose metabolism was up-regulated at the late seed developmental stage, which might explain the high sucrose content of 2mlpa soybeans. Furthermore, 604 genes related to defense mechanisms were differentially expressed between 2mlpa and 2MWT. In this study, we detected a low PA content as well as changes to multiple metabolites in the 2mlpa mutant. These results may help elucidate the regulation of metabolic events in 2mlpa. Many genes involved in PA metabolism may contribute to the substantial decrease in the PA content and the moderate accumulation of InsP3–InsP5 in the 2mlpa mutant. The other regulated genes related to photosynthesis, starch and sucrose metabolism, and defense mechanisms may provide additional insights into the nutritional and agronomic performance of 2mlpa seeds.

Potential genes and pathways along with immune cells infiltration in the progression of atherosclerosis identified via microarray gene expression dataset re-analysis

Vascular ◽  
2020 ◽  
Vol 28 (5) ◽  
pp. 643-654 ◽  
Author(s):  
Jing Xu ◽  
Yuejin Yang
Keyword(s):  
Differentially Expressed Genes ◽  
Immune Cells ◽  
Interaction Network ◽  
Wilcoxon Test ◽  
Differentially Expressed ◽  
P Value ◽  
The Novel ◽  
Microarray Gene Expression ◽  
Progression Of Atherosclerosis ◽  
Geo Database

Objective Atherosclerosis is a chronic inflammatory process characterized by the accumulation and formation of lipid-rich plaques within the layers of the arterial wall. Although numerous studies have reported the underlying pathogenesis, no data-based studies have been conducted to analyze the potential genes and immune cells infiltration in the different stages of atherosclerosis via bioinformatics analysis. Methods In this study, we downloaded GSE100927 and GSE28829 from NCBI-GEO database. Gene ontology and pathway enrichment were performed via the DAVID database. The protein interaction network was constructed via STRING. Enriched hub genes were analyzed by the Cytoscape software. The evaluation of the infiltrating immune cells in the dataset samples was performed by the CIBERSORT algorithm. Results We identified 114 common upregulated differentially expressed genes and 22 common downregulated differentially expressed genes. (adjust p value < 0.01 and log FC ≥ 1). A cluster of 10 genes including CYBA, SLC11A1, FCER1G, ITGAM, ITGB2, CD53, ITGAX, VAMP8, CLEC5A, and CD300A were found to be significant. Through the deconvolution algorithm CIBERSORT, we analyzed the significant alteration of immune cells infiltration in the progression of atherosclerosis with the threshold of the Wilcoxon test at p value <0.05. Conclusions These results may reveal the underlying correlations between genes and immune cells in atherosclerosis, which enable us to investigate the novel insights for the development of treatments and drugs.

scholarly journals Transcriptome profiling of posterior kidney of brown trout, Salmo trutta, during proliferative kidney disease

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Arun Sudhagar ◽  
Reinhard Ertl ◽  
Gokhlesh Kumar ◽  
Mansour El-Matbouli
Keyword(s):  
Immune System ◽  
Kidney Disease ◽  
Differentially Expressed Genes ◽  
Brown Trout ◽  
Salmo Trutta ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Proliferative Kidney Disease ◽  
Immune System Process ◽  
Upregulated Genes

Abstract Background Tetracapsuloides bryosalmonae is a myxozoan parasite which causes economically important and emerging proliferative kidney disease (PKD) in salmonids. Brown trout, Salmo trutta is a native fish species of Europe, which acts as asymptomatic carriers for T. bryosalmonae. There is only limited information on the molecular mechanism involved in the kidney of brown trout during T. bryosalmonae development. We employed RNA sequencing (RNA-seq) to investigate the global transcriptome changes in the posterior kidney of brown trout during T. bryosalmonae development. Methods Brown trout were exposed to the spores of T. bryosalmonae and posterior kidneys were collected from both exposed and unexposed control fish. cDNA libraries were prepared from the posterior kidney and sequenced. Bioinformatics analysis was performed using standard pipeline of quality control, reference mapping, differential expression analysis, gene ontology, and pathway analysis. Quantitative real time PCR was performed to validate the transcriptional regulation of differentially expressed genes, and their correlation with RNA-seq data was statistically analyzed. Results Transcriptome analysis identified 1169 differentially expressed genes in the posterior kidney of brown trout, out of which 864 genes (74%) were upregulated and 305 genes (26%) were downregulated. The upregulated genes were associated with the regulation of immune system process, vesicle-mediated transport, leucocyte activation, and transport, whereas the downregulated genes were associated with endopeptidase regulatory activity, phosphatidylcholine biosynthetic process, connective tissue development, and collagen catabolic process. Conclusion To our knowledge, this is the first RNA-seq based transcriptome study performed in the posterior kidney of brown trout during active T. bryosalmonae development. Most of the upregulated genes were associated with the immune system process, whereas the downregulated genes were associated with other metabolic functions. The findings of this study provide insights on the immune responses mounted by the brown trout on the developing parasite, and the host molecular machineries modulated by the parasite for its successful multiplication and release.

scholarly journals RNA-Seq Analysis of Prickled and Prickle-Free Epidermis Provides Insight into the Genetics of Prickle Development in Red Raspberry (Rubus ideaus L.)

Agronomy ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1904 ◽  
Author(s):  
Archana Khadgi ◽  
Courtney A. Weber
Keyword(s):  
Differentially Expressed Genes ◽  
Expression Patterns ◽  
Rubus Idaeus ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
Sequencing Analysis ◽  
Red Raspberry ◽  
Specialty Crop ◽  
Rubus Species ◽  
R2r3 Myb

Red raspberry (Rubus idaeus L.) is a globally commercialized specialty crop with growing demand worldwide. The presence of prickles on the stems, petioles and undersides of the leaves complicates both the field management and harvesting of raspberries. An RNA sequencing analysis was used to identify differentially expressed genes in the epidermal tissue of prickled “Caroline” and prickle-free “Joan J.” and their segregating progeny. Expression patterns of differentially expressed genes (DEGs) in prickle-free plants revealed the downregulation of some vital development-related transcription factors (TFs), including a MIXTA-like R2R3-MYB family member; MADS-box; APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) and NAM, ATAF1/2 and CUC2 (NAC) in prickle-free epidermis tissue. The downregulation of these TFs was confirmed by qRT-PCR analysis, indicating a key regulatory role in prickle development. This study adds to the understanding of prickle development mechanisms in red raspberries needed for utilizing genetic engineering strategies for developing prickle-free raspberry cultivars and, possibly, other Rubus species, such as blackberry (Rubus sp.) and black raspberry (R. occidentalis L.).

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